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Merge pull request #295 from broadinstitute/dr_remove_PrintReads_ds_argument 

PrintReads: remove -ds argument
This commit is contained in:
Mark DePristo 2013-06-19 10:55:10 -07:00
parent 573ecadecc 23ee192d5e
commit fb114e34fe
1 changed files with 2 additions and 9 deletions
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11
public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java
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@ -96,7 +96,7 @@ import java.util.*;
* -T PrintReads \ * -T PrintReads \
* -o output.bam \ * -o output.bam \
* -I input.bam \ * -I input.bam \
* -ds 0.25 * -dfrac 0.25
* </pre> * </pre>
* *
*/ */
@ -124,12 +124,6 @@ public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> impleme
@Argument(fullName = "number", shortName = "n", doc="Print the first n reads from the file, discarding the rest", required = false) @Argument(fullName = "number", shortName = "n", doc="Print the first n reads from the file, discarding the rest", required = false)
int nReadsToPrint = -1; int nReadsToPrint = -1;
/**
* Downsamples the bam file by the given ratio, printing only approximately the given percentage of reads. The downsampling is balanced (over the entire coverage)
*/
@Argument(fullName = "downsample_coverage", shortName = "ds", doc="Downsample BAM to desired coverage", required = false)
public double downsampleRatio = 1.0;
/** /**
* Only reads from samples listed in the provided file(s) will be included in the output. * Only reads from samples listed in the provided file(s) will be included in the output.
*/ */
@ -237,8 +231,7 @@ public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> impleme
nReadsToPrint--; // n > 0 means there are still reads to be printed. nReadsToPrint--; // n > 0 means there are still reads to be printed.
} }
// if downsample option is turned off (= 1) then don't waste time getting the next random number. return true;
return (downsampleRatio == 1 || random.nextDouble() < downsampleRatio);
} }
/** /**